Related papers: Implicit Solvation Using the Superposition Approxi…
In a multiscale modeling approach, we present computer simulation results for a rectifying bipolar nanopore on two modeling levels. In an all-atom model, we use explicit water to simulate ion transport directly with the molecular dynamics…
Finite element simulations of frictional multi-body contact problems via conformal meshes can be challenging and computationally demanding. To render geometrical features, unstructured meshes must be used and this unavoidably increases the…
We present an analytic approximation model for non-rigid point set registration, grounded in the multivariate Taylor expansion of vector-valued functions. By exploiting the algebraic structure of Taylor expansions, we construct a structured…
Markov Chain Monte Carlo (MCMC) underlies both statistical physics and combinatorial optimization, but mixes slowly near critical points and in rough landscapes. Parallel Tempering (PT) improves mixing by swapping replicas across…
Using new scaling parameters $\beta_i$, we derive simple expressions for the excess thermodynamic properties of the Mean Spherical Approximation (MSA) for the ion-dipole mixture. For the MSA and its extensions we have shown that the…
Aqueous lithium chloride solutions up to very high concentrations were investigated in classical molecular dynamics simulations. Various force fields based on the 12-6 Lennard-Jones model, parametrized for non-polarizable water solvent…
We demonstrate that with two small modifications, the popular dielectric continuum model is capable of predicting, with high accuracy, ion solvation thermodynamics in numerous polar solvents, and ion solvation free energies in…
The response of polar solvents to ions and polar molecules dictates many fundamental molecular processes. To understand such electrostatically-driven solvation processes, one ideally would probe the dielectric response of a solvent to an…
Implicit solvent models, such as Poisson-Boltzmann models, play important roles in computational studies of biomolecules. A vital step in almost all implicit solvent models is to determine the solvent-solute interface, and the solvent…
With the advance of supercomputers we can now afford simulations with very large ranges of scales. In astrophysical applications, e.g. simulating Solar, stellar and planetary atmospheres, interstellar medium, etc; physical quantities, like…
We present a non-conforming least squares method for approximating solutions of second order elliptic problems with discontinuous coefficients. The method is based on a general Saddle Point Least Squares (SPLS) method introduced in previous…
We present a new algorithm for isothermal-isobaric molecular-dynamics simulation. The method uses an extended Hamiltonian with an Andersen piston combined with the Nos'e-Poincar'e thermostat, recently developed by Bond, Leimkuhler and Laird…
We introduce a field-theoretic electrolyte model composed of structured solvent molecules and salt ions coupled by electrostatic and hard-core interactions. Within this explicit solvent theory, we characterize the salt-driven dielectric…
An improved numerical solver for the unified solution of compressible and incompressible fluids involving interfaces is proposed. The present method is based on the CIP-CUP (Cubic Interpolated Propagation / Combined, Unified Procedure)…
In this paper we combine a flexible covariant formulation of the shallow water equations with the semi-implicit numerical scheme developed over the years by Casulli and collaborators. After adopting an orthogonal, but non-orthonormal,…
Continuous pseudo-labeling (PL) algorithms such as slimIPL have recently emerged as a powerful strategy for semi-supervised learning in speech recognition. In contrast with earlier strategies that alternated between training a model and…
In this article we develop an algorithm for the efficient simulation of electrolytes in the presence of physical boundaries. In previous work the Discrete Ion Stochastic Continuum Overdamped Solvent (DISCOS) algorithm was derived for triply…
Compression is a crucial solution for data reduction in modern scientific applications due to the exponential growth of data from simulations, experiments, and observations. Compression with progressive retrieval capability allows users to…
Implicit particle-in-cell codes offer advantages over their explicit counterparts in that they suffer weaker stability constraints on the need to resolve the higher frequency modes of the system. This feature may prove particularly valuable…
Surface-subsurface flow models for hydrological applications solve a coupled multiphysics problem. This usually consists of some form of the Richards and shallow water equations. A typical setup couples these two nonlinear partial…